Hidden Secrets
by ChaosEngaged
Summary: Sometimes it’s better if things stay hidden, because when they are exposed life can only get worse.
1. Chapter 1 Past, Present, Future

Title: Hidden Secrets  
Author: BloodOrigen  
Spoilers: Rising  
Disclaimer: I don't any of these characters…but if David Hewlett would like to donate himself and his character Rodney McKay to the Michelle foundation…be my guest.  
Summary: Sometimes it's better if things stay hidden, because when they are exposed life can only get worse.

Chapter 1 – Past, Present, Future

Death, Destruction, Plague. As he looked around the destructed area all he could feel was sadness. A piece of rubble skipped along the broken stone as his foot moved, broken stone that he had created with his own hands and mind. Technically this broken stone shouldn't be here. That little piece of rubble shouldn't skip across other rocks, and those columns shouldn't be standing over in that distance. This area should have been destroyed with the rest of it. A black hole should be here where this planet currently stood. He didn't understand how it was still here.

He wondered why he was here. How he got here because for a fact he knew he did not walk through the Stargate. Quickly blue eyes scanned the destroyed area and a sudden pain flashed across them. This was his mistake and Atlantis was pointing it out to him. She was showing him what went wrong and pleading with him to fix it, but this was one thing he did not know how to fix. He did not know how to revive an entire civilization. He did not know what he could do anymore.

Carefully he walked down the rubble following the directions Atlantis was giving him. As he walked he thought about all the secrets he hid from the people who cared about him…but Atlantis knew them all.

When he was 10 he realized that he was adopted. He didn't stumble across his adoption papers like other kids did, nor was he told, instead he did the impossible…he moved things with his mind. At 10 he was classified as a genius but it didn't take a genius to know he was different, so he suppressed it, and never told anyone that he knew…but Atlantis did.

Seven years later, he was in university. He couldn't decide what to do. Everyone though thought he wanted to do maths or basic physics but what he really wanted to do was wander the stars. Something was compelling him to do that. He remembered when he was 10 and when he did the impossible. He decided to compromise with everyone and his heart, he went into astrophysics. No one was any wiser…but Atlantis was.

While in university he found he liked men better than women. He liked both but at times he was immediately drawn to certain men. He was a genius, he had an attitude, he had a gift, but being bi would have been too much for his "friends" to handle. So he hid it from most people, and no one was any wiser…but Atlantis was.

As he finished University, he was hired by the United States Government and more secrets were kept. He was put away into an office in Area 51; an area no one was to know existed. He was assigned to work on a project that he could never imagine but when asked where he worked by people he could never say. So he started to lie and the lies started to fall seamlessly from his lips, and no one was any wiser…but Atlantis was.

Finally he was called to look at the thing he had studied for years. He walked into the mountain with the air of an expert. His awe for the structure in front of him was carefully hidden but his eyes betrayed him and his heart felt like he was nearly home. He didn't know why. Before he could figure that out though he had realized that he had failed his primary task. He also realized that he did not understand the Stargate as well as he thought and that reality was different than theory. No one thought he realized that, but he was a genius and almost nothing eluded him. But he didn't correct anyone, and never told a soul, but Atlantis knew.

He was shipped to Siberia, where once again he was put in an office alone. In Siberia he learned quickly that being different was bad. He was no novice to abuse, verbal or physical, but this could be considered cruel and unusual punishment. He was given tasks to learn what things do, to give his mind menial tasks which he must complete. The cold did nothing to speed up his work. Neither did the broken fingers, broken toes, broken ribs or black eyes but he got it done and hid the pain. And when an object came into his grasp and lit up at the slightest thought he suppressed it, because being different was bad and he was hurt enough as it is. He hid all this from everyone, but Atlantis knew and wept for him when she learned.

Once again he was called forth to help out with the Stargate. He still didn't know why. He screwed up the last time, that he knew, why would they give him a second chance. But he took it with all the hope he had left, because this could be his life line to get out of the hole he was in, but once again it went wrong. Everything went wrong for him. It was only thanks to another man that he was able to see what needed to be done. This time though he was giving a parting, a tiny bit of hope to hold on to, but then he was shipped back, back to the pain and back to the humility that he was shown in Siberia. This was a place he had no respect, but this time he had hope and he hang on to that by burring it deep inside of him and Atlantis saw what he did and silently rejoiced at what she saw.

After the pain of Siberia, he was sent to Antarctica. It was pleasantly warm compared to Siberia but he still kept his guards up. Any sort of trust he held for people was gone and it would take a lot for him to gain it back again. In the confines of his own workspace things lit up around him with a simple touch of his mind but he only did this when someone with an ATA gene was around. He still didn't want to seem different even though it was obvious that was ok here. His gift which would have been praised was hidden, and Atlantis still wept for her charge and beloved.

Then John Sheppard walked into his life and his delusions of hiding his gift were shattered. All it took was one view of those stars that he wanted to wander for so long and the feeling of going home had come back to him. He knew now for a fact that it was okay to be different and let his genius roam free for moments at a time proving to everyone that he was as smart as he said he was. Now though a new element was being added…friendship, and he can remember the last time he had friends and the pain he went through when they left him. So he hid his emotions away in his mind and pretended he didn't care, but Atlantis knew the truth.

As he stood before the Stargate, before his trip to Atlantis, the feeling of going home washed over him. He heard each chevron snap into place and a sort of happiness fell over him. The walk through the Stargate was exhilarating and gave him a rush of adrenaline and when he stepped onto Atlantis his senses came alive and he could feel her waking from her deep slumber, lightly prodding at his mind. And as the city rose from its ocean grave, he heard a whisper across his mind "Welcome home my beloved" but he never told anyone he could communicate with a long forgotten city.


	2. Interlude: Atlantis POV

Title: Hidden Secrets  
Author: BloodOrigen  
Spoilers: Rising  
Disclaimer: I don't any of these characters…but if David Hewlett would like to donate himself and his character Rodney McKay to the Michelle foundation…be my guest.  
Summary: Sometimes it's better if things stay hidden, because when they are exposed life can only get worse.  
Authors note: Thought I might add this until I finish the next chapter...

Interlude: From the depths she watches

Atlantis watched on as her beloved walked through the halls, looking at everything in wonder and awe. He was so much like her previous occupants, like her creators, but he had been abused so much it made her mental components weep. Her beloved was so closed up, so guarded, that it would take a lot of work to break down those barriers that had been built up. She lit up for him and him alone. The others thought it was for the one, whose genetic makeup they knew was close to her former occupants, what did the call him? Oh that's right Major John Sheppard but to her he was more of a protector. She would need his help eventually with her beloved but not right now. It was her job to get him out of his shell, to let his natural genius shine like his ancestors had.

Sometimes she wonders how he did it, how he hid his gene and history from everyone, how that doctor did not see what he was hiding. But then she realizes, it is another one of his barriers. The human mind is complex, she realizes, almost as complex as her. It has created those barriers to protect itself, like the shield that she has that covers her city, but know those barriers must be broken.

She starts by slowly speaking to him, whispering things in his mind when he lets his guard down. She whispers words of comfort and words of praise. She makes sure he remembers to eat and forces him to leave his labs once n awhile. The other sub programs under her have taken a liking to him too. He fixes them with a skill that the others don't have. At times he even makes them run better than they already had. He doesn't' use his own gene. It has been suppressed but the potential for it to awaken is great. She watches as the doctor injects him with something. He thinks it gives his patients the ATA gene but it reality it awakens the recessive ones. For her beloved though it breaks down the barrier he has created on it and finally she can sense him completely. It will take awhile for his gene to become unsuppressed fully and his true potential to be discovered but she is happy because the first step has been taken.


	3. Discoveries Once Found

**Chapter 2 – Discoveries once found…**

Pain reverberated through the stones as he touched them. Just because the life signs detector hadn't picked up on anything didn't mean that there wasn't anything living on these planets. There was life alright and it screamed with the agony of 1000 tortured souls. Each on tortured beyond the point of recognition. Life that he promised he would never hurt, but he had hurt both people and these creatures.

He walked down a set of stairs still intact. Amazing how one structure can survive the test of time, but then again none of what he was experiencing was supposed to exist. It wasn't supposed to be here standing, not only time but the destruction of 2/3 of a solar system and the trust that people in Atlantis held for him and now he had failed them again.

Wait, failed them again? What was he talking about? Something was missing from his mind. There was something there but he just couldn't grasp it. It was to far back, hidden by other memories.

He remembers when he first stepped into Atlantis and when the city rose from her slumber. Things continuously were lighting up before he could get to them. He sees what has happened, why the city is empty before anyone else does. It is all flashing to him in the coding of the city. The coding tells him everything the hologram doesn't and even more. It tells him of the wraith and how long the war had gone on for. She shows him location after location of where the Atlantians had been and gone, her previous tenets. He wonders why he can decipher this at a moments glance. The others seem to be ignoring it, and the scientists he had hand picked are skipping right past it. He doesn't tell anyone about his discovery, choosing to reveal it if they ask, but something else is whispering to him. Something is whispering to him that they are too young to understand, and Rodney thinks he has gone insane but Atlantis knows he hasn't.

He remembers when he found the rooms filled with scientific equipment. He was with Sheppard at the time, the first time after the chair incident that he had been with this man. It was awkward walking down the hall with him. They had been walking in complete silence when a door suddenly flung open revealing the treasure trove within. He walks in first forgetting for a moment that Sheppard was behind him. As he walked in he felt a presence brush across his mind and he stopped, saying one word "Mine". He noticed Sheppard shifting his gun and giving him a weary look. Rodney turned to face him and then put one hand to his communicator announcing that they had found the science labs and then ordering the other scientists to pick desks and sort out the clutter. But the lab that he had walked into first, he kept for himself. The room itself glowed with pride because of who she was owned by and Rodney felt good that he had shared his discovery but kept the secret of his connection to Atlantis still a secret for he was still afraid of how everyone would react and he didn't want to be alone again. For that Atlantis stayed by his side all night, making sure he was never alone.

Later he noticed that after certain periods of time, mostly when everyone had gone to bed, his projects would either be frozen or terminated. The first time it happened he tried everything to get the project back running but nothing happened. He then proceeded to hit the wall and sparks flew directly at him. When he finally decided to leave the lab, in his sleep deprived state, he was always directed to a transporter. Before he even touched the screen he was either near the mess or right by his room. Most of the time he didn't even process that it had happened and usually walked out in a sort of daze. On those instances he usually felt like someone was laughing at him, but then he would shake his head and convince himself he was imagining it. Atlantis though just laughed at his antics and kept her other secrets for another day.

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Authors Note: Ok ok...i know this one is quite short...but i have had inspirations with the next "chapter" which will be another Atlantis POV and it's the ancient shield chapter and the getting together of the Mckay, Sheppard team :P I always though Atlantis had a part in that...

Ok and now to thank the reviews which for the first two chapter were: Shakia, Reefgirl, Angw  
-Thank You SOOO much for clicking that little button down there that says review.  
-As for Atlantis we will be seeing alot of her thoughts...i mean why can't a city think for herself :D


	4. Smiles and Shields

Authors Note: cringes at upset fans I know…I know…I haven't updated To Save a Shattered Soul…but I've had mid-semester exams and I've been trying to be good by studying for once. I promise during these two weeks that I have off I will get some chapters away from screaming fans

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**Chapter 3 – Smiles and Shields (Atlantis POV)**

She watched as he walked among those broken halls. Each stone he saw cracked caused him to cringe and she saw how it weighted on his mind. Right now he needed a friend, a comfort, but the man within her walls who fit that description was wallowing in his own guilt and lashing out against him.

She understood why one did not want to see the other but she had put them together for a reason. They were there to help each other, not to destroy each others soul with guilt. Atlantis then remembered how she put them together in the first place.

Her beloved had been so happy when he received the gene therapy, as she was too. Finally his natural gene that his mind had locked away was being released. Now she could help him relax. She laughed though when his face lit up as he put on the shield, that her previous inhabitants had designed, but also realized that he was alone in his discovery.

Silently she whispered in his mind 'Follow me' and he followed without question, like a child doing as a mother had told.

It was finally time for her other protector to come into play and when she lead them to each other she knew she was right. Both of them had received hard lives, but seeing them together made her laugh and her halls brighten. These two, she could see, were going to be a pair of, what these people called…umm…clowns. They would be a source of ever lasting amusement and besides…they complemented each other. They would guard each others backs; one would not fall without the other.

Both of them were positively bouncing now with the thought of something new. If this was going to happen every time, Atlantis though her interfaces would explode from the rush of energy she received. It was defiantly going to be a wild ride with these two. First her protector poked her beloved, then shoved, and then punched. Each time the green light spread across her beloved's body. Her protector's smile grew larger, and so did hers. Then he shot her beloved.

If Atlantis had a heart she was sure it would have stopped. Time slowed as she saw the bulled head towards him. Sure her creators had tested the shield out against their own weapons but never against weapons as primitive as her current occupants wielded.

The bullet hit the shield and for a split second, as the bullet tumbled to the ground, the power flowing through the city stopped. When Atlantis finally looked again she let a laugh ring through Rodney's mind. He looked like a gapping water mammal, not unlike what these people called whales.

Wait…

they had another saying for this…

what was it...

oh that's right…

fish…

he looked like a gaping fish.

A great, big, gaping fish. This was a lot like what her current occupants watched in her recreational room. It was called a comedy skit.

Her protector was bouncing up and down now, which was an odd sight indeed. Her beloved though was still in shock.

"You shot me"

"Uh-huh" Sheppard said with a child like innocence.

"You," he paused between words, "shot me"

Sheppard nodded rapidly. Rodney looked at his leg and grinned.

"Amazing"

Suddenly Rodney was out the door with Sheppard on his heels. Atlantis watched as they made their way to the balcony, in the gate room. Everyone looked confused as they entered. On the one hand was their normally calm military leader and on the other hand was the man, they called the devil himself, their head of science. They might have been confused but Atlantis wasn't. She knew exactly what they were going to do and she also saw the bond that had formed between the two of them. She hoped it would never break.

The bond though didn't break, it shattered on both ends. This time Atlantis knew the bond would have to be stronger. Stronger than anything else that had formed between her walls, but first she would need to learn, learn what was keeping their shields up…when they were together.

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Ok I'm planning a Sheppard chapter...but i don't know when...umm...might be awhile as i really need to get in the right mind frame to right sheppard. But a Rodney chapter should be up soon...i hope...


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